Genocrunch in Docker

A Dockerfile to run Genocrunch web application on Docker.

Resources

• Git clone URL: https://github.com/genocrunch/genocrunch-docker.git
• Documentation: https://github.com/genocrunch/genocrunch-docker
• Docker image https://hub.docker.com/r/genocrunch/genocrunch-docker
• Genocrunch documentation: https://github.com/genocrunch/genocrunch
• Genocrunch official web site: https://genocrunch.epfl.ch

Rights

• License: MIT (See LICENSE.txt for details)

System requirements

• docker: https://docs.docker.com
• git: https://git-scm.com/

Installation (on Debian linux)

If not done yet, install docker by following the documentation at https://docs.docker.com/install.

Note: you will have to use sudo with docker commands if docker is not configured to be used as a non-root user. You may have to contact your IT administrator for that.

The Genocrunch web application will need to store some data files and to use a database. To avoid data loses when updating a container, you can set both data storage location and database on the host (as opposed to set it up on the docker container itself).

Set the Genocrunch data storage location

Create a new data storage directory on the host side. This directory will be used by the Genocrunch web app running on the docker container:

$ mkdir /path/to/genocrunch/storage

Set the Genocrunch database

Create a PostgreSQL database on the host side. This database will be used by the Genocrunch web app running on the docker container:

$ sudo apt-get install postgresql postgresql-contrib
$ sudo su postgres
$ psql
postgres=# create role genocrunch_user with login password 'genocrunch_db_password';
postgres=# create database genocrunch owner genocrunch_user;
postgres=# \q
$ exit

Then, allow the docker container to be listened from the database by modifying the /etc/postgresql/9.?/main/postgresql.conf file as following:

#/etc/postgresql/9.?/main/postgresql.conf 
...
listen_addresses = '*'
...

Also add the following line to /etc/postgresql/9.?/main/pg_hba.conf:

#/etc/postgresql/9.?/main/pg_hba.conf 
...
host    all             all             0.0.0.0/0               md5 
...

Finally, restart the PostgreSQL service:

$ sudo /etc/init.d/postgresql restart

Get the docker image

To get the docker image, you can either Pull the docker image from dockerhub or Build the docker image from the Dockerfile.

If you want a pre-build docker image with a default Genocrunch installation, pull it directly from dockerhub. Building the image from the Dockerfile allows you to setup aa docker image with a custom installation of Genocrunch.

Pull the docker image from dockerhub

If you want a pre-build docker image with a default Genocrunch installation, pull it from the genocrunch/genocrunch-docker dockerhub repository:

$ docker pull genocrunch/genocrunch-docker:1.0.0

Although the docker image comes with default configuration, you will later be able to use the -v argument in the docker run command to customize the configuration by specifying custom configuration files.

You can get configuration files templates from the config directory of the https://github.com/genocrunch/genocrunch-docker repository. Here are three options to download these files:

• Get a full copy of the repository using git clone:

$ git clone https://github.com/genocrunch/genocrunch-docker.git

The configuration files will then be located in the genocrunch-docker/config directory.

• Download the config directory only using the DownGit tool here.

• Download the configuration files one by one, following this example:

$ wget https://raw.githubusercontent.com/genocrunch/genocrunch-docker/master/config/config.yml

Build the docker image from the Dockerfile

Download the Dockerfile from its git repository:

$ git clone https://github.com/genocrunch/genocrunch-docker.git

Before building a docker image using the Dockerfile, you may want to edit the Dockerfile in order to customize the installation of the Genocrunch web app. For this, open genocrunch-docker/Dockerfile with your favorite editor and add the following lines:

USER genocrunch_user
WORKDIR /home/genocrunch_user/genocrunch

# Additional link(s) that should be included in the Infos menu of the topbar (set to [] to ignore)
RUN sed -i 's/info_links:.*$/info_links: [{name: "link_name", href: "link_url", target: "_blank"}]/g' config/config.yml

# Webmaster email
RUN sed -i 's/webmaster_email:.*$/webmaster_email: webmaster_email/g' config/config.yml

# Google analytics tag (set to "" to ignore)
RUN sed -i 's/gtag_id:.*$/gtag_id: your_google_analytics_tag_id/g' config/config.yml

# Send a validation link to user email to confirm registration?
RUN sed -i 's/user_confirmable:.*$/user_confirmable: false/g' config/config.yml

# Compressed archive format for downloading an archive of analysis files. Valid choices are zip or tar.gz
RUN sed -i 's/archive_format:.*$/archive_format: zip/g' config/config.yml

# Max time without update for a job owned by a guest user not to be automatically deleted by the 'cleanup' rake task (in days)
RUN sed -i 's/max_sandbox_job_age:.*$/max_sandbox_job_age: 2/g' config/config.yml

# Max time without update for a job owned by a registered user not to be automatically deleted by the 'cleanup' rake task (in days)
RUN sed -i 's/max_job_age:.*$/max_job_age: 365/g' config/config.yml

# Set the email address to be used by the web app:
RUN sed -i 's/config.mailer_sender =.*$/config.mailer_sender = "[email protected]"/g' config/initializers/devise.rb
RUN sed -i 's/config.action_mailer.default_url_options =.*$/config.action_mailer.default_url_options = {:host => "localhost:3000"}/g' config/environments/development.rb
RUN sed -i 's/:address =>.*$/:address => "smtp.gmail.com",/g' config/environments/development.rb
RUN sed -i 's/:port =>.*$/:port => 587,/g' config/environments/development.rb
RUN sed -i 's/:domain =>.*$/:domain => "mail.google.com",/g' config/environments/development.rb
RUN sed -i 's/:user_name =>.*$/:user_name => "[email protected]",/g' config/environments/development.rb
RUN sed -i 's/:password =>.*$/:password => "app_email_password",/g' config/environments/development.rb
RUN sed -i 's/:authentication =>.*$/:authentication => :plain,/g' config/environments/development.rb
RUN sed -i 's/:enable_starttls_auto =>.*$/:enable_starttls_auto => true/g' config/environments/development.rb

# Set the database name, user and password (must match host settings described above):
RUN sed -i 's/database:.*$/database: genocrunch/g' config/database.yml
RUN sed -i 's/^.*username:.*$/  username: genocrunch_user/g' config/database.yml
RUN sed -i 's/^.*password:.*$/  password: genocrunch_db_password/g' config/database.yml

Finally, build the docker image using the docker build command:

$ docker build --rm -t genocrunch/genocrunch-docker .

Initialize the database

Complete the installation of the Genocrunch web app by initializing its database from within a docker container using rails schema (db/schema.rb) and seeds (db/seeds.rb). Caution: this will overwrite the database and should be applied only for initialization/re-initialization, not updates. For updates, use migrations or SQL queries.

If you have pulled the image from dockerhub and the default database configuration does not match the configuration on the host, you can use the -v argument in the docker run command to specify custom configuration files as following:

-v path/to/config/config.yml:/home/genocrunch_user/genocrunch/config/config.yml
-v path/to/config/initializers/devise.rb:/home/genocrunch_user/genocrunch/config/initializers/devise.rb
-v path/to/config/environments/development.rb:/home/genocrunch_user/genocrunch/config/environments/development.rb
-v path/to/config/database.yml:/home/genocrunch_user/genocrunch/config/database.yml

# Run a docker container in interactive mode:
# Replace /path/to/genocrunch/storage by the appropriate path (see the Set the Genocrunch data storage location section above).
# Replace host.ip.address by the host ip address.
# If needed, add custom configuration files using the -v argument as described above.
$ docker run -v /path/to/genocrunch/storage:/home/genocrunch_user/genocrunch/users -p 3000:3000 --add-host=hostaddress:host.ip.address -it genocrunch/genocrunch-docker bash

# Initialize the database:
$ rails db:schema:load

# To change default guest and admin passwords, emails and storage quotas, edit the `User.create` query in the db/seeds.rb file with nano:
$ nano db/seeds.rb

# Finally, seed the database:
$ rails db:seed

# You can finally close the container:
$ exit

Usage

Run a docker container using the command below. Make sure to replace /path/to/genocrunch/storage with the appropriate path (see the Set the Docker container external resources section above) and replace host.ip.address by the host ip address. This will automatically start the Genocrunch web server which will be accessible in a web browser at http://localhost:3000 on the host and host.ip.address:3000 on your network.

Note: Remember that if you have pulled the image from dockerhub, you can use the -v argument in the docker run command to specify custom configuration files.

# Replace /path/to/genocrunch/storage by the appropriate path (see the Set the Genocrunch data storage location section above).
# Replace host.ip.address by the host ip address.
# If needed, add custom configuration files using the -v argument as described in the Initialize the database section above.
$ docker run -v /path/to/genocrunch/storage:/home/genocrunch_user/genocrunch/users -p 3000:3000 --add-host=hostaddress:host.ip.address -it genocrunch/genocrunch-docker

Contributing

Thank you for your interest in contributing. Get started here.